Some type of carry over.
Depending on the variety and type of malt gray protein mud can form. Certain types of malt produce tan/brown mud. European Pils malt is an example of malt that forms gray mud, wheat is another example. There is nothing wrong with the malt. Boiling isn't the issue. If protein mud does not form on top of the grain bed it ends up in the bottle. The brewing process needs to be improved or adjusted for the malt. Any type of carry over has a negative impact on stability, balance and quality of the final product.
Copper and Clorox are a no-no. Wort creates a shield over copper which protects the copper from oxidation and changing color, patina. Bleach removes the protective covering. Circulate boiling water through the cooler to clean it.
High side oxidation can occur during mashing, as well. Slopping hot brewing water into malt and stirring it up to kill the evil dough balls can inject enough air into the mash to cause oxidation when temps are above 140F, and the wort will darken during boiling. However, wort at times will darken during boiling and oxidation isn't the reason for it darkening. When using high quality malt and a fine brewing method, wort lightens up during the boil. The finer the brewing method, along with using high quality ingredients the higher in quality the final product will be.